The amount is the "largest defamation damages award in Australian legal history," Wilson's lawyers said.
The judgment follows a unanimous jury verdict in June that Bauer Media, publisher of Woman's Day magazine, had defamed Wilson by branding her a "serial liar" who "fabricated almost every aspect of her life."
The magazine published articles claiming Wilson lied about her name, age and childhood so she could make it in Hollywood. As a result, the actress said, she missed out on several prominent film roles and other opportunities in the wake of the success of "Pitch Perfect 2," which came out in May 2015.
Justice John Dixon said Bauer Media had failed to show the claims made about Wilson were substantially true or trivial.
In a series of tweets, Wilson said the judgment was the "end of a long and hard court battle against Bauer Media who viciously tried to take me down with a series of false articles."
"This case wasn't about the money," she wrote. "I'm looking forward to helping out some great Australian charities and supporting the Oz film industry with the damages I've received."
The $3.6 million in damages is the biggest defamation payout in Australian history, Wilson's lawyers said.
It was broken down into $522,000 ($650,000 Australian) in general damages, and $3.1 million ($3.9 million Australian) in special damages for Wilsons' "opportunity for new screen roles lost by reason of the defendant's publications."
Dixon defended the high payout as necessary to vindicate the actress.
"Unless substantial damages are awarded there is a real risk that the public will not be convinced of the seriousness of the defamation, but will rather wrongly conclude that the articles were trivial or not that serious," he told the court.
Bauer Media, Dixon added, failed to properly investigate the allegations, which came from a source who required payment and anonymity, and whom the editor considered "had an ax to grind."
In a statement, Bauer Media said it was "considering today's judgment."
The company's general counsel Adrian Gross said Bauer Media "has a long history of delivering great stories to our readers and we have a reputation for developing some of the best editorial teams in this country."
Wilson's lawyer, Richard Leder, said judge's decision "recognizes the serious harm caused to Rebel's reputation and held Bauer Media to account for what the judge accepted was an orchestrated campaign against her."